Introduction

I sequenced the complete insert of the pDNA library of pMT06. I already extracted all sequences in front of the 3’ adapter from the sequences data and added counts to identical sequences by starcode. I now want to make an overview about how many pDNA insert sequences in the pDNA still match the designed inserts.

Identify those barcodes that are attached to a wrong insert

Clearly wrongly assigned barcodes can be assigned to the correct insert Barcodes that are attached to a mixed population of inserts should to be excluded from any analysis where this plasmid library was used

Barcode re-evaluation

Investigate the mutational load of the barcodes with a good match

# # Export barcodes that are attached to multiple inserts
# bc_exclude <- matching_df_exclude$barcode %>% unique()
# write.csv(bc_exclude, "/DATA/usr/m.trauernicht/projects/tf_activity_reporter/data/SuRE_TF_1/pDNA_seq/bc_exclude.csv")
# 
# # Export barcodes that are attached to the wrong insert
# bc_replace <- pDNA_seq_incorrect %>% dplyr::select(barcode, `bc-match`, `insert-match`) %>% unique()
# write.csv(bc_replace, "/DATA/usr/m.trauernicht/projects/tf_activity_reporter/data/SuRE_TF_1/pDNA_seq/bc_replace.csv")

Session Info

paste("Run time: ",format(Sys.time()-StartTime))

## [1] "Run time:  50.97526 secs"

getwd()

## [1] "/DATA/usr/m.trauernicht/projects/SuRE_deep_scan_trp53_gr/pDNA_insert_seq"

date()

## [1] "Wed Dec  9 14:20:37 2020"

sessionInfo()

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] shiny_1.4.0                 tibble_3.0.1               
##  [3] plotly_4.9.2.1              LncFinder_1.1.4            
##  [5] sunburstR_2.1.4             d3r_0.9.0                  
##  [7] vwr_0.3.0                   latticeExtra_0.6-29        
##  [9] lattice_0.20-38             stringdist_0.9.5.5         
## [11] ggbeeswarm_0.6.0            ggplot2_3.3.0              
## [13] dplyr_0.8.5                 readr_1.3.1                
## [15] tidyr_1.0.0                 phylotools_0.2.2           
## [17] ape_5.4-1                   maditr_0.6.3               
## [19] plyr_1.8.6                  ShortRead_1.42.0           
## [21] GenomicAlignments_1.20.1    SummarizedExperiment_1.14.1
## [23] DelayedArray_0.10.0         matrixStats_0.55.0         
## [25] Biobase_2.44.0              Rsamtools_2.0.3            
## [27] GenomicRanges_1.36.1        GenomeInfoDb_1.20.0        
## [29] Biostrings_2.52.0           XVector_0.24.0             
## [31] IRanges_2.18.3              S4Vectors_0.22.1           
## [33] BiocParallel_1.18.1         BiocGenerics_0.30.0        
## [35] seqinr_3.6-1               
## 
## loaded via a namespace (and not attached):
##  [1] colorspace_1.4-1       hwriter_1.3.2          ellipsis_0.3.0        
##  [4] class_7.3-15           farver_2.0.1           prodlim_2019.11.13    
##  [7] lubridate_1.7.4        codetools_0.2-16       splines_3.6.3         
## [10] knitr_1.30             ade4_1.7-13            jsonlite_1.7.1        
## [13] pROC_1.16.1            caret_6.0-85           png_0.1-7             
## [16] compiler_3.6.3         httr_1.4.1             fastmap_1.0.1         
## [19] assertthat_0.2.1       Matrix_1.2-18          lazyeval_0.2.2        
## [22] later_1.1.0.1          htmltools_0.5.0        tools_3.6.3           
## [25] gtable_0.3.0           glue_1.4.2             GenomeInfoDbData_1.2.1
## [28] reshape2_1.4.4         Rcpp_1.0.5             vctrs_0.2.4           
## [31] nlme_3.1-143           crosstalk_1.0.0        iterators_1.0.12      
## [34] timeDate_3043.102      gower_0.2.1            xfun_0.19             
## [37] stringr_1.4.0          mime_0.9               lifecycle_0.2.0       
## [40] zlibbioc_1.30.0        MASS_7.3-51.5          scales_1.1.0          
## [43] ipred_0.9-9            promises_1.1.1         hms_0.5.3             
## [46] RColorBrewer_1.1-2     yaml_2.2.1             rpart_4.1-15          
## [49] stringi_1.5.3          foreach_1.4.7          e1071_1.7-4           
## [52] lava_1.6.6             rlang_0.4.8            pkgconfig_2.0.3       
## [55] bitops_1.0-6           evaluate_0.14          purrr_0.3.3           
## [58] labeling_0.3           recipes_0.1.9          htmlwidgets_1.5.2     
## [61] tidyselect_1.1.0       magrittr_1.5           R6_2.5.0              
## [64] generics_0.0.2         pillar_1.4.3           withr_2.1.2           
## [67] prettydoc_0.4.0        survival_3.1-8         RCurl_1.95-4.12       
## [70] nnet_7.3-12            crayon_1.3.4           rmarkdown_2.5         
## [73] jpeg_0.1-8.1           grid_3.6.3             data.table_1.12.8     
## [76] ModelMetrics_1.2.2.1   digest_0.6.27          xtable_1.8-4          
## [79] httpuv_1.5.4           munsell_0.5.0          beeswarm_0.2.3        
## [82] viridisLite_0.3.0      vipor_0.4.5